Colonel Jorge Mendonca told the Baha Mousa inquiry that claims he punched an Iraqi prisoner in front of more than 100 troops were false. Photograph: Barry Batchelor/PA

A former army commanding officer said today that he knew nothing about alleged abuse of Iraqi detainees by his men.

Colonel Jorge Mendonca said he was not informed of a series of incidents in which prisoners were reportedly ill-treated by soldiers under his command in Iraq in 2003.

Giving evidence to the public inquiry into the death of hotel worker Baha Mousa, he suggested that his officers might have kept him "out of the loop" because of his "reputation for doing things properly".

Mendonca also strongly denied a claim by a witness that he punched an Iraqi prisoner in front of more than 100 troops.

Mousa, 26, was working as a receptionist at Basra's Ibn al-Haitham hotel when it was raided by British forces looking for weapons.

He and several colleagues were arrested and taken to the base of 1st Battalion the Queen's Lancashire Regiment (1QLR), where he died on 15 September 2003, having suffered 93 separate injuries.

Today, the inquiry heard details of a string of other occasions when members of 1QLR allegedly assaulted or abused Iraqi detainees. The incidents reported by other witnesses included:

• British troops being told to hit prisoners being transported in the back of armoured vehicles if they tried to talk.

• Iraqis being "casually slapped" if they did not do what they were told.

• A 12-year-old boy being kicked in the head for throwing a stone at British soldiers.

• An officer telling junior soldiers to beat up detainees.

• An Iraqi prisoner left with a broken wrist and concussion after being assaulted by British troops.

• A sergeant boasting that he had kicked a suspected Iraqi thief in the throat.

• Pictures taken of a bare-chested British soldier grabbing the hair of one of a number of prisoners with masking tape bound around his head.

Mendonca, who was commanding officer of 1QLR at the time, told the inquiry he was not informed about any of these incidents.

He said: "There is, of course, the possibility that, because I had, I think, a very clear reputation for doing things properly, that some officers might have thought that was a reason for me to be kept out of the loop on things. But it isn't a correct reason, and it shouldn't happen."

Counsel to the inquiry Gerard Elias QC, asked whether his officers might have feared getting a "bollocking" if they reported abuse by their men.

Mendonca replied: "Had he reported it to me, then he wouldn't be getting the bollocking."

Elias asked him: "If indeed – and it will be a matter, of course, not for me but for the inquiry – there were a significant number of assaults and ill-treatment of detainees across the companies and across the period of time of your involvement in Basra, that would tend, wouldn't it, to point to a systematic problem?"

Mendonca answered: "If there was a large number of incidents across all the companies, then yes, it would."

A former member of 1QLR, identified as S038, told the inquiry last month that he saw Mendonca punch an Iraqi prisoner in the side of the face and call him a "terrorist fucker" in front of about 120 troops. He told the inquiry: "I was disgusted. A CO [commanding officer] is supposed to lead by example."

Elias asked Mendonca today: "Did any such incident as you punching a detainee in front of a large number of men actually occur?"

He replied: "Absolutely never."

Mendonca went on: "I was the commanding officer of the battalion, and if I punched someone I would expect the battalion to be talking about it and the brigade commander would have found out. They knew everything else we were doing."

He admitted that his soldiers had not received enough training in handling prisoners before they deployed to Iraq.

"I don't think we spent enough time on prisoner-handling," he said. "With hindsight, I'm sure we didn't spend enough time on prisoner-handling. We also weren't aware that civilian detainees were going to be a major feature of the tour."

Mendonca was awarded the Distinguished Service Order for his "inspirational" leadership during the Preston-based 1QLR's tour of duty in Iraq in 2003. But he became the most senior British officer to face a court martial in recent history when he was charged with negligently performing a duty in relation to the abuse of Mousa and other prisoners.

He was cleared in February 2007 and left the army several months later.